Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate 200453 SO1275 succinate-semialdehyde dehydrogenase (NCBI ptt file)
Query= SwissProt::O06837 (502 letters) >FitnessBrowser__MR1:200453 Length = 482 Score = 306 bits (784), Expect = 1e-87 Identities = 182/474 (38%), Positives = 261/474 (55%), Gaps = 10/474 (2%) Query: 19 LPHQMLIGGQWVNAQSDKTLNVYNPATGDTLTDVPDGDVEDVNAAVESAAATLQSDAWRR 78 L Q I GQW +A S +T+ + NPATG + VP + AA+ +A A L AWR Sbjct: 9 LRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALP--AWRA 66 Query: 79 MPPSARERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWATK 138 + R L R +LL + D+LA L T GK L +K EV +A ++ + A A + Sbjct: 67 LTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKG-EVTYAASFIEWFAEEAKR 125 Query: 139 LTGSTLDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLK 198 + G T+ R + PVGV AAI PWNFP M K APALA G T+V+K Sbjct: 126 IYGDTIP-----GHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVK 180 Query: 199 PAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRI 258 PA +TP TAL LA LA AG+PAG +V+TG G+ + +P V K++FTGST VG Sbjct: 181 PAPQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIK 240 Query: 259 IGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHES 318 + + C +LK +SLELGG +P IV D + A EGA A + N GQ C +R+YV Sbjct: 241 LMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300 Query: 319 IYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTE 378 +Y++ ++L++ + VG G+ GV GP+++ E V H+ + I+ GA ++ GG Sbjct: 301 VYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKV 360 Query: 379 APCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASI 438 FF +PT+ N + K +R+ +E FGP+ F+D+ +V+ +AN + +GL A Sbjct: 361 HELGGNFF-EPTVLTNAD-KSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYF 418 Query: 439 WTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHY 492 + D+S ++ + LE G V VNT + PFGG K SG+GRE IE Y Sbjct: 419 YGRDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEY 472 Lambda K H 0.317 0.134 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 537 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 502 Length of database: 482 Length adjustment: 34 Effective length of query: 468 Effective length of database: 448 Effective search space: 209664 Effective search space used: 209664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory